Hi Joshua,
You can retrieve this information from the Table Browser (from main
page, click on "Tables" on the top blue navigation bar). After selecting
a clade, genome, and assembly of your choice, set the following:
group: Genes and Gene Prediction Tracks
track: choose a gene prediction track you would like to use (I'll use
'UCSC Genes' for this example)
table: the default table will be the primary table for that track
('knownGene' in this case)
region: click 'define regions', on the following page you may paste (or
upload a file) of up to 1000 regions. Click 'submit'.
output format: selected fields from primary and related tables
output file: enter a filename to save your results to a file, or leave
blank to display results in the browser
Click 'get output'. On the following page, select the appropriate fields
('name' for example) then click 'get output'.
More information on how to use the Table Browser can be found here:
http://genome.ucsc.edu/cgi-bin/hgTables#Help
Please contact us again at [email protected] if you have any further
questions.
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
qcshare wrote:
> Dear Dr. Mary,
>
> Could you please tell me how to annotate some sequences, and get the
> information which gene this sequence belongs to?
> I only have sequences physical start/end positions, and don't have ATCG
> sequence information, the sequence length could be short (eg.40bp) or
> long(2000bp).
>
> There are more than 500 sequences need to be annotated, so can I use UCSC
> Genome Brower or Galaxy to perform annotation for a large number of sequence
> at one time?
>
> Thanks very much.
>
> Your Sincerely,
>
> Joshua.
> On Tue, Sep 28, 2010 at 12:36 PM, Mary Goldman <[email protected]> wrote:
>
>
>> Hi Joshua,
>>
>> The easiest way to download all the CpG Islands with their coordinates and
>> names is to use the table browser (http://genome.ucsc.edu/cgi-bin/hgTables).
>> First, select the clade, genome and assembly of interest. Next, select
>> "Regulation" from the group pull-down menu and "CpG Islands" from the track
>> pull-down menu. Select "selected fields from primary and related tables" as
>> the output format, enter a name for the output file if you would like (leave
>> blank to keep output in browser), and click "get output". Select the
>> "chrom", "chromStart", "chromEnd" and "name" check boxes and click "get
>> output".
>>
>> I hope this information is helpful. Please feel free to contact the mail
>> list again if you require further assistance.
>>
>> Best,
>> Mary
>> ------------------
>> Mary Goldman
>> UCSC Bioinformatics Group
>>
>>
>> On 9/27/10 9:07 PM, qcshare wrote:
>>
>>
>>> Dear Professor,
>>> I want to download the genome CpG islands information, such as the number
>>> of
>>> chromosome, start/end position of the CpG islands and CpG islands ID
>>> numbers, I just found the first three items, but I can not found the
>>> information of CpG islands ID numbers.
>>> Could you please tell me where can I get this information?
>>>
>>> Thank you very much!
>>>
>>> Your Sincerely!
>>>
>>> Joshua.
>>> _______________________________________________
>>> Genome maillist - [email protected]
>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>>
>>>
>>>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
